Try Dunbrack's lab page, specifically S2C:
http://dunbrack.fccc.edu/Guoli/s2c/index.php
ASTRAL also offers ATOM-based database of sequences, but unfortunately only for PDB entries present in SCOP (lags a year or two behind PDB):
http://astral.berkeley.edu/scopseq-1.73.html
At 02:33 AM 5/28/2008, Florian Odronitz wrote: >Hi Modelleros, > >I am in the process of modeling ~100 similar structures. I have a >bunch of templates that cover most of the sequence of the targets. >However, there are some gaps. Most gaps are loop regions or contain >loops, sometimes comprising ~30 aas, so ab initio modeling is not an >option. So I go to the PDB and BLAST with my missing sequence as a >query. I get a great number of hits but for most of the PDBs, the >large parts of the sequence have no _structure_. Downloading each of >those PDBs and looking at them is not an option since its hundreds. >I am looking for a tool to BLAST (or otherwise search) the sequences >in the PDB that have _structure_. The people at the PDB told me there >is no such option and they are not aware of such an resource. >I figure I am not the first person to encounter such a difficulty. How >would you handle this? Is there such a resource? > >Thanks and best regards, >Florian >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage
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